rs1019271

chr4-13786692-A-Gchr4-13786692-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_121681.1(LINC01182):n.282-43088A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,870 control chromosomes in the GnomAD database, including 24,955 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (24955 hom., cov: 31)
• Consequence: LINC01182 NR_121681.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564

Genes affected

LINC01182 (HGNC:49564): (long intergenic non-protein coding RNA 1182)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01182	NR_121681.1	n.282-43088A>G		intron_variant, non_coding_transcript_variant
LOC101929048	XR_925415.3	n.434+303T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01182	ENST00000669061.1	n.549-43088A>G		intron_variant, non_coding_transcript_variant
	ENST00000689499.2	n.182-19732T>C		intron_variant, non_coding_transcript_variant
LINC01182	ENST00000510907.5	n.282-43088A>G		intron_variant, non_coding_transcript_variant		2
	ENST00000691923.2	n.339-19732T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85056 AN: 151750 Hom.: 24946 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.594

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.560 AC: 85082 AN: 151870 Hom.: 24955 Cov.: 31 AF XY: 0.557 AC XY: 41385 AN XY: 74238

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.596

Alfa AF: 0.638 Hom.: 41977

Bravo AF: 0.550

Asia WGS AF: 0.561 AC: 1951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.3
Dann	Benign	0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1019271; hg19: chr4-13788316;